Turns out I was wrong with commit 8f612c3, and this commit seems actually fix the problem.

1 files changed, 2 insertions, 2 deletions

diff --git a/roundcubemail/program/include/rcube_imap.php b/roundcubemail/program/include/rcube_imap.php
index 00587a36d..a05dcf1aa 100644
--- a/roundcubemail/program/include/rcube_imap.php
+++ b/roundcubemail/program/include/rcube_imap.php
@@ -545,7 +545,7 @@ class rcube_imap
             if ($sql_arr = $this->db->fetch_array($sql_result))
                 return $sql_arr[0];
         }
-        list ($thread_tree, $msg_depth, $has_children) = iil_C_Thread($this->conn, $mailbox, 'REFERENCES', 'ALL');
+        list ($thread_tree, $msg_depth, $has_children) = iil_C_Thread($this->conn, $mailbox, rcmail::get_instance()->config->get('imap_thread_algorithm'), 'ALL');
         $this->update_thread_cache($mailbox, $thread_tree, $msg_depth, $has_children);
         return count($thread_tree);
     }
@@ -587,7 +587,7 @@ class rcube_imap
 
     $message_threading = $this->get_capability('thread=references') &&
                          rcmail::get_instance()->imap->threading;
-    $max = $this->_messagecount($mailbox, $message_threading ? 'THREADS' : 'ALL');
+    $max = $this->_messagecount($mailbox, 'ALL');
 
     list($begin, $end) = $this->_get_message_range($max, $page);